Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate BWI76_RS03270 BWI76_RS03270 sugar ABC transporter ATP-binding protein CymD
Query= BRENDA::Q70HW1 (384 letters) >FitnessBrowser__Koxy:BWI76_RS03270 Length = 376 Score = 360 bits (924), Expect = e-104 Identities = 198/379 (52%), Positives = 263/379 (69%), Gaps = 18/379 (4%) Query: 1 MARVLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEG 60 MA V L I K Y + V +L+I D EF VFVGPSGC K+TTLRMIAGLEDI+ G Sbjct: 1 MATVSLRKIEKRYENGFK-AVHGIDLEIHDGEFMVFVGPSGCAKSTTLRMIAGLEDISGG 59 Query: 61 NLYIGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAA 120 +YIG+R+VND+PPKDR IAMVFQNYALYPH TV+ NMAFGLK++K PK EI RRV++AA Sbjct: 60 EIYIGNRKVNDLPPKDRGIAMVFQNYALYPHKTVFDNMAFGLKMQKRPKDEIKRRVEDAA 119 Query: 121 KILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRK 180 + L+I LL RKPK +SGGQRQRVA+GRAIVR+P VFL DEPLSNLDAKLRV MR +I + Sbjct: 120 EKLEITELLYRKPKEMSGGQRQRVAVGRAIVRKPDVFLFDEPLSNLDAKLRVSMRMKIAQ 179 Query: 181 LHQRLQ-----TTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGF 235 LH+ L+ T+IYVTHDQTEA+T+GDRI V+ G I Q DTP +Y+ P N FVA F Sbjct: 180 LHRSLKEEGHPATMIYVTHDQTEALTLGDRICVLNHGNIMQVDTPTDLYNYPNNKFVASF 239 Query: 236 IGSPAMNFIRGEIVQDGDAFYFR-APSISLRLPEGRYGVLKASGAIGKPVVLGVRPE--D 292 IGSP++N I I ++ + Y AP + + +P + +L+ G I KPV G+RPE Sbjct: 240 IGSPSINLIDTAIRKNNERLYVEIAPGVEILIPHSKQVLLE--GYINKPVCFGIRPEHIS 297 Query: 293 LHDEEVFMTTYPDSVLQMQVEVVEHMGSEVYLHTSIGPNTIVARVNPRHV--YHVGSSVK 350 L ++ + T+ + VL VVE+MGSE +L+ +G ++ARV+ + + +H+G +++ Sbjct: 298 LASDDDDLNTF-EGVL----TVVENMGSEKFLYFIVGGKELIARVDTQDINPFHIGKTLR 352 Query: 351 LAIDLNKIHIFDAETEESI 369 ++ H+FD E ++ Sbjct: 353 FNLNTAFCHVFDFYNENNL 371 Lambda K H 0.321 0.138 0.395 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 441 Number of extensions: 18 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 384 Length of database: 376 Length adjustment: 30 Effective length of query: 354 Effective length of database: 346 Effective search space: 122484 Effective search space used: 122484 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory